Publications

  1. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Sep 23.
    View PubMed
  2. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014; 15:423. Epub 2014 Jun 03.
    View PubMed
  3. Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinformatics. 2014; 15(1):280. Epub 2014 Aug 15.
    View PubMed
  4. Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keles S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet. 2013 Jun; 9(6):e1003565. Epub 2013 Jun 20.
    View PubMed
  5. Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keles S, Landick R, Kiley PJ. Genome-scale Analysis of E. coli FNR Reveals Complex Features of Transcription Factor Binding. PLOS Genetics. 2013 (accepted).
  6. Wu Y, Kikuchi S, Yan H, Zhang W, Rosenbaum H, Iniguez AL, Jiang J. Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell. 2011 Nov; 23(11):4054-64. Epub 2011 Nov 11.
    View PubMed
  7. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J. 2010 May 06. [Epub ahead of print]
    View PubMed
  8. Hirsch CD, Wu Y, Yan H, Jiang J. Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species. Mol Biol Evol. 2009 Dec; 26(12):2877-85. Epub 2009 Sep 09.
    View PubMed
  9. Yan H, Talbert PB, Lee HR, Jett J, Henikoff S, Chen F, Jiang J. Intergenic locations of rice centromeric chromatin. PLoS Biol. 2008 Nov 25; 6(11):e286.
    View PubMed
  10. Neumann P, Yan H, Jiang J. The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics. 2007 Jun; 176(2):749-61. Epub 2007 Apr 03.
    View PubMed
  11. Yan H, Jiang J. Rice as a model for centromere and heterochromatin research. Chromosome Res. 2007; 15(1):77-84.
    View PubMed
  12. Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang J. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell. 2006 Sep; 18(9):2123-33. Epub 2006 Jul 28.
    View PubMed
  13. Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell. 2005 Dec; 17(12):3227-38. Epub 2005 Nov 04.
    View PubMed
  14. Lee HR, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, Jiang J. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A. 2005 Aug 16; 102(33):11793-8. Epub 2005 Jul 22.
    View PubMed
  15. Mudge J, Huihuang Y, Denny RL, Howe DK, Danesh D, Marek LF, Retzel E, Shoemaker RC, Young ND. Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering. Genome. 2004 Apr; 47(2):361-72.
    View PubMed
  16. Yan HH, Mudge J, Kim DJ, Shoemaker RC, Cook DR, Young ND. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome. 2004 Feb; 47(1):141-55.
    View PubMed
  17. Yan HH, Mudge J, Kim DJ, Larsen D, Shoemaker RC, Cook DR, Young ND. Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theor Appl Genet. 2003 May; 106(7):1256-65. Epub 2003 Jan 25.
    View PubMed
  18. Foster-Hartnett D, Mudge J, Larsen D, Danesh D, Yan H, Denny R, Penuela S, Young ND. Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. Genome. 2002 Aug; 45(4):634-45.
    View PubMed
  19. Yan HH, Liu GQ, Cheng ZK, Li XB, Liu GZ, Min SK, Zhu LH. A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization, localization, and introgression to O. sativa. Theor Appl Genet. 2002 Feb; 104(2-3):177-83.
    View PubMed
  20. Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC. Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome. 2001 Aug; 44(4):572-81.
    View PubMed
  21. Cheng Z, Yan H, Yu H, Tang S, Jiang J, Gu M, Zhu L. Development and applications of a complete set of rice telotrisomics. Genetics. 2001 Jan; 157(1):361-8.
    View PubMed
  22. Yan HH, Liu GQ, Cheng ZK, Min SK, Zhu LH. Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by using RFLP analysis and genomic in situ hybridization. Genome. 2001; 44:86-95.
  23. Chen C, Yan H, Zhai W, Zhu L, Sun J. Identification and chromosomal location of a new tandemly repeated DNA in maize. Genome. 2000 Feb; 43(1):181-4.
    View PubMed
  24. Cheng ZK, Yu HX, Yan HH, Gu MH, Zhu LH. B chromosome in a rice aneuploid variation. Theor Appl Genet. 2000; 101:564-8.
  25. Liu GQ, Yan HH, Fu Q, Qian Q, Zhang ZT, Zhai WX, Zhu LH. Mapping of a new gene for brown planthopper resistance transferred from Oryza eichingeri. Chinese Science Bulletin. 2000; 46:1459-61.
  26. Cheng ZK, Yan HH, Yu HX, Qian Q, Yi CD, Gu MH, Zhu LH. Fast assignment of DNA sequences to individual chromosome arms based on dosage effects from a set of rice telotrisomics. Acta Bot Sin. 2000; 42:708-11.
  27. Zhai W, Chen H, Yan H, Yan C, Wang G, Zhu L. Analysis and location of a rice BAC clone containing telomeric DNA sequences. Sci China C Life Sci. 1999 Feb; 42(1):68-73.
    View PubMed
  28. Yan HH, Cheng ZK, Liu GQ, Chen CX, Min SK, Zhu LH. Identification of Oryza sativa x Oryza officinalis F1 and backcross progenies using genomic in-situ hybridization [Chinese]. Chinese J of Genet. 1999; 26:53-58.
  29. Cheng ZK, Yan HH, Gu MH. The descending order of chromosomal length and the numbering system of rice chromosome. Hereditas (Beijing) [Chinese]. 1999; 21:46-9.
  30. Yan HH, Min SK, Zhu LH. Visualization of Oryza eichingeri chromosomes in intergenomic hybrid plants from O. sativa x O. eichingeri via fluorescent in situ hybridization. Genome. 1999; 42:48-51.
  31. Liu GQ, Yan HH, Luo YW, Min SK, Zhu LH. RFLP analysis of euploid plants from cross between Oryza sativa and Oryza eichingeri [Chinese]. Chinese J Rice Sci. 1999; 13:129-33.
  32. Cheng ZK, Yan HH, Dang BY, Hu ZM, Gu MH, Zhu LH. Microdissection and amplification of the chromosome arm 5S in a rice telotetrasomic. Chinese Science Bulletin. 1998; 43:590-4.
  33. Cheng ZK, Yan HH, Dang BY, Hu ZM, Gu MH, Zhu LH. Microdissection and amplification of the chromosome arm 5S in a rice telotetrasomic [Chinese]. Chinese Science Bulletin. 1998; 43:272-6.
  34. Yan HH, Hu HY, Zhang XQ, Zhang ZT, Tian SL, Xiong ZM, Min SK. Cytogenetical studies on the pollen-derived plants from interspecific hybrid in genus Oryza [Chinese]. Acta Agronomica Sinica. 1997; 23:689-92.
  35. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Fu Q. The production and cytogenetical studies of Oryza sativa-Oryza eichingeri amphiploid. Chinese Journal of Genetics. 1997; 24:23-9.
  36. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Fu Q. The production and cytogenetical studies of Oryza sativa-Oryza eichingeri amphiploid [Chinese]. Chinese Journal of Genetics. 1997; 24:30-5.
  37. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Tang S. The transfer of planthopper resistance from Oryza eichingeri to Oryza sativa. Chinese Journal of Genetics. 1997; 24:277-84.
  38. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Tang S. The transfer of planthopper resistance from Oryza eichingeri to Oryza sativa [Chinese]. Chinese Journal of Genetics. 1997; 24:424-31.
  39. Yan HH, Hu HY, Fu Q, Yu HY, Tang S, Xiong ZM, Min SK. Morphological and cytological studies of the hybrid between Oryza sativa and Oryza officinalis [Chinese]. Chinese J Rice Sci. 1996; 10:138-42.